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Nat Commun. 2020 Jan 14;11(1):253. doi: 10.1038/s41467-019-14213-y.

Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan.

Author information

1
Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark.
2
Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsucho, Sakyo-ku, Kyoto, 606-8501, Japan.
3
Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
4
Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata, 950-2181, Japan.
5
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna B(VBC), 1030, Vienna, Austria.
6
Faculty of Agriculture, University of Miyazaki, Gakuen-Kibanadainishi 1-1, Miyazaki, 889-2192, Japan.
7
Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, 292-0818, Japan.
8
Department of Chemistry and Bioscience, Section for Biotechnology, Aalborg University, 9220, Aalborg, Denmark.
9
Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
10
National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, 8210, Aarhus V, Denmark.
11
Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan. shuseis@ige.tohoku.ac.jp.
12
Bioinformatics Research Centre, Aarhus University, 8000, Aarhus C, Denmark. mheide@birc.au.dk.
13
Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark. sua@mbg.au.dk.

Abstract

Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here, we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with colonization of Japan by Lotus japonicus over the past ~20,000 years. Based on patterns of genomic variation, we infer the details of the colonization process where L. japonicus gradually spread from subtropical conditions to much colder climates in northern Japan. We identify genomic regions with extreme genetic differentiation between northern and southern subpopulations and perform population structure-corrected association mapping of phenotypic traits measured in a common garden. Comparing the results of these analyses, we find that signatures of extreme subpopulation differentiation overlap strongly with phenotype association signals for overwintering and flowering time traits. Our results provide evidence that these traits were direct targets of selection during colonization and point to associated candidate genes.

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